It’s a former Mafia slaughterhouse where God — and not the Godfather — calls the shots now.

A Brooklyn building that once housed the infamous Gemini Lounge — where Gambino crime-family soldiers carried out countless, unspeakable mob murders — has become the Flatlands Church of God, drawing faithful every Sunday to sing praises to the Almighty.

Donald Williams, pastor of the mob killing-field-turned-Pentecostal church at Flatlands and Troy avenues, said he didn’t know his church site’s gruesome history before paying $220,000 for it in 1997.

The two-story brick building is where Gambino soldier Roy DeMeo and his crew of Mafia psychopaths whacked and dismembered anywhere from 70 to 200 victims in the 1970s and early ’80s, according to prosecutors.

But Williams said he doesn’t regret buying the property — even as the church now struggles years later to stay afloat and raise money for necessary repairs.

“I think God sent us here for a reason,” Williams said. “After we opened, many of our neighbors said our coming was a sigh of relief. They said if a church is here, God is here, and they could finally sleep at night.”

The pastor also said he believes the church’s presence has saved souls of people murdered there.

The church’s altar and seating area for its 100 members was once a smoke-filled dance floor at the old lounge.

An elevated stage, now used for a public address system, is where DeMeo usually sat and kept a safe to stash loan-shark money, guns and other valuables.

And a side apartment, now used for church offices, was where unsuspecting victims were lured and killed in an execution style dubbed the “Gemini Method.”

The system was designed to eliminate messiness, prosecutors say.

Someone would shoot the victim once in the head and then wrap a towel around his wound like a turban to stem blood flow. Another person would then stab the victim in the chest to divert more blood from pumping out of the gunshot wound.

Before being tossed in bags and boxes and dropped at a local dump, the corpse would be chopped up in a basement room the church has since converted into a computer room and some bathrooms.

It was “an assembly line procedure,” said Walter Mack Jr., a former federal prosecutor who tried and helped convict some of DeMeo’s crew.

“People went to the Gemini Lounge and never returned.”

The pastor and his wife, Sarah, said they learned many of the building’s gruesome details after reading the 1993 book, “Murder Machine,” by Gene Mustain and Jerry Capeci. It documents the tales of DeMeo, who is believed to have been whacked himself in 1983.

“I read most of it, but not all — it’s too gory,” Williams said.

Capeci, who operates ganglandnews.com, said he’s glad to see a more peaceful use of the site.

“No matter how evil or corrupt a place is, it’s never too late to start anew,” he said.